Ramaraj, T. | Search bioRxiv

bioRxiv2022

The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication

Gossypium herbaceum is a species of cotton native to Africa and Asia that is one of the two domesticated diploids. Together with its sister-species G. arboreum, these A-genome taxa represent models of the extinct A-genome donor of modern polyploid cotton, which provide about 95% of cotton grown worldwide. As part of a larger effort to characterize variation and improve resources among diverse diploid and polyploid cotton genomes, we sequenced and assembled the genome of G. herbaceum cultivar (cv) Wagad, representing the first domesticated accession for this species. This chromosome-level genome was generated using a combination of PacBio long-read technology, HiC, and Bionano optical mapping and compared to existing genome sequences in cotton. We compare the genome of this cultivar to the existing genome of wild G. herbaceum subspecies africanum to elucidate changes in the G. herbaceum genome concomitant with domestication, and extend these analyses to gene expression using available RNA-seq. Our results demonstrate the utility of the G. herbaceum cv Wagad genome in understanding domestication in the diploid species, which could inform modern breeding programs.

genomics↗

bioRxiv2021

Dual domestication, diversity, and differential introgression in Old World cotton diploids

Domestication in the cotton genus is remarkable in that it has occurred independently four different times at two different ploidy levels. Relatively little is known about genome evolution and domestication in the cultivated diploid species Gossypium herbaceum and G. arboreum, because of the absence of wild representatives for the latter species, their ancient domestication, and their joint history of human-mediated dispersal and interspecific gene flow. Using in-depth resequencing of a broad sampling from both species, we confirm their independent domestication, as opposed to a progenitor-derivative relationship, showing that diversity (mean {pi} = 2.3x10-3) within species is similar, and that divergence between species is modest (weighted FST=0.4430). Individual accessions were homozygous for ancestral SNPs at over half of variable sites, while fixed, derived sites were at modest frequencies. Notably, two chromosomes with a paucity of fixed, derived sites (i.e., chromosomes 7 and 10) were also strongly implicated in introgression analyses. Collectively, these data demonstrate variable permeability to introgression among chromosomes, which we propose is due to divergent selection under domestication and/or the phenomenon of F2 breakdown in interspecific crosses. Our analyses provide insight into the evolutionary forces influencing diversity and divergence in the diploid cultivated species, and establish a foundation for understanding the contribution of introgression and/or strong parallel selection to the extensive morphological similarities shared between species. Significance statementThe cotton genus (Gossypium) contains four different species that were independently domesticated at least 4,000 years ago. Relatively little is understood about diversity and evolution in the two diploid African-Asian sister-species G. herbaceum and G. arboreum, despite their historical importance in the region and contemporary cultivation, largely in the Indian subcontinent. Here we address questions regarding the relationship between the two species, their contemporary levels of diversity, and their patterns of interspecific gene flow accompanying their several millennia history of human-mediated dispersal and contact. We validate independent domestication of the two species and document the genomic distribution of interspecific genetic exchange.

evolutionary biology↗